Retroviruses exist as infectious viruses and as endogenous retroviral copies (ERVs) which are viral DNA copies integrated into host DNA. Such ERVs are a permanent part of the host genome and represent 8-10% of host chromosomal DNA. Retroviruses were first recognized as naturally occurring infectious agents linked to various neoplasms in their host species. We have been engaged in an ongoing effort to characterize pathogenic viruses, and identify the various host factors that restrict the replication cycle of these viruses. Mouse leukemia viruses (MLVs) are gammaretroviruses linked to induction of neoplasms and to neurological and immunodeficiency diseases. Inbred strains of laboratory mice and wild mouse species differ in their susceptibility to mouse gammaretrovirus infection and to virus-induced diseases, and they also differ in the types of MLVs that they carry. Susceptibility differences are due to variations in specific host genes, and we have been engaged in an ongoing effort to identify and characterize host genes that are either involved in virus resistance or that contribute to the disease process. There are two types of host genes involved in virus-induced disease. First, the mouse genome contains copies of mouse gammaretrovirus genomes, many of which can produce infectious and pathogenic viruses. Second, there are also host factors that interfere directly with virus infection and replication, and we are particularly interested in those factors that inhibit virus entry and the early post-entry stages of the virus replicative cycle. These host factors affect different stages of the viral life cycle. At the level of entry, resistance can be caused by polymorphisms in the cell surface receptors. After the gammaretrovirus enters the receptive cell, reverse transcription and translocation to the nucleus can be inhibited or altered by virus resistance factors Fv1, mApobec3, and TRIM5alpha. Our group aims to characterize the endogenous retroviruses carried in the mouse genome, and the host encoded resistance factors and their viral targets. Our ultimate goal is to describe co-evolutionary patterns of virus-host interactions in natural populations. This work relies heavily on wild mice because laboratory strains provide only a limited sampling of the genetic diversity in Mus. Also, wild mouse species allow us to examine survival strategies in natural populations that harbor virus and to follow the evolution of the resistance genes. These mice additionally provide a source of novel resistance genes and virus variants. One set of projects aims to identify viral and cell receptor determinants responsible for virus binding and entry. We are currently working on the XPR1 receptor for the xenotropic/polytropic MLVs (XP-MLVs). We have determined that, in mouse populations exposed to infectious virus, virus resistance is mediated by polymorphisms of the cell surface receptor. We have identified a total of six XPR1 susceptibility variants in wild mice and described the geographic and species distribution of these Mus Xpr1 variants. Five of these receptors restrict entry by two or more of the virus host range variants that rely on XPR1, and all of these receptors evolved in populations exposed to X-MLVs. Virtually all mammalian species have a functional XPR1 receptor and can be infected by X-MLVs. In our most recent study on X/P-MLV entry, we shifted our attention from restrictive receptors to the permissive XPR1 receptors that mediate entry of all X/P-MLVs. Most Mus species and some laboratory strains carry the permissive Xpr1-sxv allele, and there are other XPR1 receptors in various non-rodent mammalian species that are fully permissive despite considerable sequence variation in the receptor-determining regions. We examined permissive cells from four mammalian species (Mus dunni, human, mink, rabbit) in virus interference assays to determine if 9 different X/P-MLV isolates use the same of different receptor determinants in these 4 polymorphic, but fully permissive receptors. Results showed that some viruses produce distinctive species-specific interference profiles that can, in some cases, be correlated with specific receptor sequence variations. This suggests these MLV variants evolved to adapt to host receptor polymorphisms, to circumvent blocks by competing viruses or to avoid host-encoded envelope glycoproteins acquired for defense. In another series of experiments we characterized pathogenic and nonpathogenic MLVs of polytropic host range. Ecotropic, xenotropic and polytropic mouse leukemia viruses (E-, X-, P-MLVs) exist in mice as infectious viruses and as ERVs. All 3 MLV subgroups are linked to leukemogenesis, which involves generation of recombinants with polytropic host range. Although P-MLVs are deemed to be the proximal agents of disease induction, few biologically characterized infectious P-MLVs have been sequenced for comparative analysis. We analyzed the complete genomes of 16 naturally occurring infectious P-MLVs, 12 of which were typed for pathogenic potential. We sought to identify ERV progenitors, recombinational hotspots, and segments that are always replaced, never replaced, or linked to pathogenesis or host range. Each P-MLV has an E-MLV backbone with P- or X-ERV replacements that together cover 100% of the recombinant genomes, with different substitution patterns for X- and P-ERVs. Two segments are always replaced, in envelope (Env): the N-terminus of the surface subunit, and the cytoplasmic tail R peptide. Viral gag gene replacements are influenced by host restriction genes Fv1 and Apobec3. Pathogenic potential maps to the env transmembrane subunit segment encoding the N-heptad repeat (HR1). Molecular dynamics simulations identified three novel interdomain salt bridges in the lymphomagenic virus HR1 that could affect structural stability, entry or sensitivity to host immune responses. The long terminal repeats of lymphomagenic P-MLVs are differentially altered by recombinations, duplications or mutations. This analysis of the naturally occurring, sometimes pathogenic P-MLV recombinants defines the limits and extent of intersubgroup recombination, and identifies specific sequence changes linked to pathogenesis and host interactions. Another ongoing study is in the process of characterizing a novel 8.0 kb endogenous retrovirus, XTERV-LS, that we identified in the amphibian, Xenopus tropicalis. This ERV has intact open reading frames for all viral proteins, but has an unusual genomic structure and domain relationships to known retroviruses. Phylogenetic analysis failed to identify close relationships with known retroviruses and XTERV-LS is distinct from the 2 previously described X. tropicalis ERVs: XTERV-LS1 and Xen-1. The reverse transcriptase domain of this ERV shows closest similarity to the ancient env-deficient ERV-L family of endogenous retroviruses, and to the exogenous spumaviruses confirming an evolutionary relationship between these subgroups. The TM domain of the XTERV-LS env clusters with the mammalian syncytin genes that function in trophoblast fusion in placenta formation. This newly acquired retrovirus provides a link between the ancient ERV-L and spumaviruses as well as a connection to the retrovirus Env genes captured as syncytins.